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Overview of population samples included in genetic analyses of Pleuromamma xiphias (Plankton Population Genetics)

Overview of population samples that were included in genetic analyses of Pleuromamma xiphias from across the Atlantic Ocean. Specimens were collected on the Atlantic Meridional Transect 22 (AMT22) cruise on RRS James Cook from Oct-Nov 2012. Data columns include collection location and date, ocean biome, number of individuals sampled (N), number of haplotypes observed (H), the ratio of haplotypes to sample size (H/N), haplotype diversity (h) and nucleotide diversity (π) for each site. 'Pop' indicates whether the sample was included in population genetic analyses (Yes/No, see Goetze et al. 2016 for explanation).

In summary (excerpted from above):
Bulk plankton samples were collected on Atlantic Meridional Transect Cruise 22 (AMT22) between 10/13/2012 and 11/19/2012. Oblique tows were conducted with bongo nets (200 um, 333 um), towed between on average 324 m depth and the sea surface. A General Oceanics flowmeter (2030RC) mounted in the mouth of the 200 um net was used to measure seawater filtered during the tow. Plankton from the 200 um mesh net was bulk preserved immediately in 100% ethyl alcohol, the alcohol was changed to fresh within 12–24 h of collection, and samples were stored at -20 C. Plankton from the 333 um mesh net was sorted live at sea, and Pleuromamma xiphias specimens were preserved immediately in RNALater (Ambion), followed by cryopreservation in liquid nitrogen, and long-term storage at -80 C.

Specimens included in the genetic analyses in this study were collected at 18 stations, located between 39 38.82N and 40 4.39S latitude. The majority of genetic analyses focused on stations with sufficient sample size for population-level inference (N > 42), including AMT22-09 through AMT22-29 and AMT22-45 through AMT22-68. Specimens used in genetic analyses were primarily RNALater-preserved, but some specimens were included from ethanol-preserved samples to achieve the minimum target sample size of 45 individuals per station. When a major genetic break across the equatorial region was identified, we included samples from stations AMT22-31 through AMT22-43 to assess the genetic composition of populations across this region. Population-level analyses were not conducted on these latter stations due to small sample sizes and low abundance in this region, but sequences from these animals were included in the haplotype network. DNA was extracted from individual P. xiphias adults using the DNeasy Blood & Tissue kit (Qiagen), following the manufacturer’s protocol, with the exception of longer elution incubation times (Goetze, 2011). The second of two elutions for each individual was used in this study. Polymerase Chain Reaction (PCR) amplification of a 681-bp fragment of mtCOI was conducted with primers and PCR and sequencing protocols as described in (Goetze, 2011). Forward and reverse sequences from each individual were aligned and checked for errors in Geneious (v7.1.8, Biomatters). Consensus sequences for all individuals were aligned using MUSCLE (Edgar, 2004), and unique mtCOI haplotypes were identified using FABox (http://users-birc.au.dk/biopv/php/fabox/). MtCOI sequences representing unique haplotypes are available under GenBank accession numbers KT429028–KT429159. A minimum spanning haplotype network was inferred for all mtCOI sequences using Population Analysis with Reticulate Trees (PopART; http://popart.otago.ac.nz), in order to investigate geographic patterns in the distribution of haplotypes across the Atlantic.

A Bongo Net consists of paired plankton nets, typically with a 60 cm diameter mouth opening and varying mesh sizes, 10 to 1000 micron. The Bongo Frame was designed by the National Marine Fisheries Service for use in the MARMAP program. It consists of two cylindrical collars connected with a yoke so that replicate samples are collected at the same time. Variations in models are designed for either vertical hauls (OI-2500 = NMFS Pairovet-Style, MARMAP Bongo, CalVET) or both oblique and vertical hauls (Aquatic Research). The OI-1200 has an opening and closing mechanism that allows discrete "known-depth" sampling. This model is large enough to filter water at the rate of 47.5 m3/minute when towing at a speed of two knots. More information: Ocean Instruments, Aquatic Research, Sea-Gear

PI supplied instrument name: bongo net

Dataset-specific description

Oblique tows were conducted with bongo nets (200 um, 333 um), towed between on average 324 m depth and the sea surface.

General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.